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Abstract Nylanderia(Emery) is one of the world's most diverse ant genera, with 123 described species worldwide and hundreds more undescribed. Fifteen globetrotting or invasive species have widespread distributions and are often encountered outside their native ranges. A molecular approach to understanding the evolutionary history and to revision ofNylanderiataxonomy is needed because historical efforts based on morphology have proven insufficient to define major lineages and delimit species boundaries, especially where adventive species are concerned. To address these problems, we generated the first genus‐wide genomic dataset ofNylanderiausing ultraconserved elements (UCEs) to resolve the phylogeny of major lineages, determine the age and origin of the genus, and describe global biogeographical patterns. Sampling from seven biogeographical regions revealed a Southeast Asian origin ofNylanderiain the mid‐Eocene and four distinct biogeographical clades in the Nearctic, the Neotropics, the Afrotropics/Malagasy region, and Australasia. The Nearctic and Neotropical clades are distantly related, indicating two separate dispersal events to the Americas between the late Oligocene and early Miocene. We also addressed the problem of misidentification that has characterized species‐level taxonomy inNylanderiaas a result of limited morphological variation in the worker caste by evaluating the integrity of species boundaries in six of the most widespreadNylanderiaspecies. We sampled across ranges of species in theN. bourbonicacomplex (N. bourbonica(Forel) + N. vaga(Forel)), theN. fulvacomplex (N. fulva(Mayr) + N. pubens(Forel)), and theN. guatemalensiscomplex (N. guatemalensis(Forel) + N. steinheili(Forel)) to clarify their phylogenetic placement. Deep splits within these complexes suggest that some species names – specificallyN. bourbonicaandN. guatemalensis– each are applied to multiple cryptic species. In exhaustively samplingNylanderiadiversity in the West Indies, a ‘hot spot’ for invasive taxa, we found five adventive species among 22 in the region; many remain morphologically indistinguishable from one another, despite being distantly related. We stress that overcoming the taxonomic impediment through the use of molecular phylogeny and revisionary study is essential for conservation and invasive species management. 

Abstract Fungus‐farming ants (Hymenoptera: Formicidae) have become model systems for exploring questions regarding the evolution of symbiosis. However, robust phylogenetic studies of both the ant agriculturalists and their fungal cultivars are necessary for addressing whether or not observed ant–fungus associations are the result of coevolution and, if so, whether that coevolution has been strict or diffuse. Here we focus on the evolutionary relationships of the species within the ant genusMyrmicocryptaand of their fungal cultivars. The fungus‐farming ant genusMyrmicocryptawas created by Fr. Smith in 1860 based on a single alate queen. Since then, 31 species and subspecies have been described. Until now, the genus has not received any taxonomic treatment and the relationships of the species within the genus have not been tested. Our molecular analyses, using ∼40 putative species and six protein‐coding (nuclear and mitochondrial) gene fragments, recoverMyrmicocryptaas monophyletic and as the sister group of the genusMycocepurusForel. The speciesM. tuberculataWeber is recovered as the sister to the rest ofMyrmicocrypta. The time‐calibrated phylogeny recovers the age of stem groupMyrmicocryptaplus its sister group as 45 Ma, whereas the inferred age for the crown groupMyrmicocryptais recovered as 27 Ma. Ancestral character‐state analyses suggest that the ancestor ofMyrmicocryptahad scale‐like or squamate hairs and that, although such hairs were once considered diagnostic for the genus, the alternative state of erect simple hairs has evolved at least seven independent times. Ancestral‐state analyses of observed fungal cultivar associations suggest that the most recent common ancestor ofMyrmicocryptacultivated clade 2 fungal species and that switches to clade 1 fungi have occurred at least five times. It is our hope that these results will encourage additional species‐level phylogenies of fungus‐farming ants and their fungal cultivars, which are necessary for understanding the evolutionary processes that gave rise to agriculture in ants and that produced the current diversity of mutualistic ant–fungus interactions.